Improve prettier fix markdownlint required workflow

Author: data-douser

SECURITY.md

@@ -1,7 +1,7 @@
-Thanks for helping make GitHub safe for everyone.
-
 # Security
 
+Thanks for helping make GitHub safe for everyone.
+
 GitHub takes the security of our software products and services seriously, including all of the open source code repositories managed through our GitHub organizations, such as [GitHub](https://github.com/GitHub).
 
 Even though [open source repositories are outside of the scope of our bug bounty program](https://bounty.github.com/index.html#scope) and therefore not eligible for bounty rewards, we will ensure that your finding gets passed along to the appropriate maintainers for remediation.

client/CLI-USAGE.md

@@ -154,7 +154,7 @@ Set the output format for `list` commands. Accepts `text` (default) or `json`.
 
 **Text Format** - Human-readable output:
 
-```
+```text
 codeql_bqrs_decode (tools/codeql_bqrs_decode) : Decode BQRS result files to human-readable formats
 ```
 
@@ -348,7 +348,7 @@ node src/ql-mcp-client.js list tools
 
 Output:
 
-```
+```text
 codeql_bqrs_decode (tools/codeql_bqrs_decode) : Decode BQRS result files to human-readable formats
 codeql_bqrs_info (tools/codeql_bqrs_info) : Get metadata and information about BQRS result files
 ...
@@ -451,7 +451,7 @@ The old CLI flags have been removed and new commands have been added:
   - New: `node src/ql-mcp-client.js` → shows help
   - To run integration tests: `node src/ql-mcp-client.js integration-tests`
 
-### New Features:
+### New Features
 
 - **`list` commands**: Discover MCP server primitives (auto-starts server if needed)
   - `list primitives` - List all primitives (prompts, resources, tools)
@@ -464,7 +464,7 @@ The old CLI flags have been removed and new commands have been added:
 - **`--format` option**: Control output format (text/json) for list commands
 - **Server auto-start**: List commands automatically start the server if not running
 
-### Script Replacement:
+### Script Replacement
 
 The new `server` commands replace the shell scripts:
 

server/ql/csharp/tools/src/PrintCFG/PrintCFG.md

@@ -1,4 +1,4 @@
-# Print CFG for C#
+# Print CFG for `csharp` Source Files
 
 Produces a representation of a file's Control Flow Graph (CFG) for specified source files.
 

server/src/prompts/document-codeql-query.prompt.md

@@ -85,12 +85,12 @@ Based on gathered context, create or update the documentation file.
 
 The documentation file (`QueryFileBaseName.md`) should follow this standardized format with these sections:
 
-**Section 1: Title and Description**
+### Section 1: Title and Description
 
 - H1 heading with the query name from @name metadata
 - One paragraph description from @description, expanded if needed
 
-**Section 2: Metadata Table**
+### Section 2: Metadata Table
 
 A table with these rows:
 
@@ -100,15 +100,15 @@ A table with these rows:
 - Precision: The @precision value
 - Tags: The @tags values
 
-**Section 3: Overview**
+### Section 3: Overview
 
 Concise explanation of what vulnerability/issue this query detects and why it matters. 2-4 sentences.
 
-**Section 4: Recommendation**
+### Section 4: Recommendation
 
 Brief guidance on how developers should fix issues flagged by this query. Include code patterns to use or avoid.
 
-**Section 5: Example**
+### Section 5: Example
 
 Two subsections:
 
@@ -117,7 +117,7 @@ Two subsections:
 
 Use the appropriate language identifier for the code blocks (e.g., `javascript`, `python`, `java`).
 
-**Section 6: References**
+### Section 6: References
 
 A list of links to:
 

server/src/prompts/ql-lsp-iterative-development.prompt.md

@@ -9,7 +9,7 @@ These "iterative" tools work entirely through file paths and numeric positions.
 Every operation is expressible as a tool call with explicit `file_path`, `line`, and `character` parameters.
 Thus, this prompt can be used in any environment where the query files are on disk, and it does not require any special editor integration.
 
-## Use This Prompt When...
+## Use This Prompt When
 
 - Exploring unfamiliar CodeQL libraries to discover available classes and predicates
 - Incrementally building a query clause-by-clause with real-time feedback

server/src/prompts/ql-tdd-advanced.prompt.md

@@ -191,6 +191,7 @@ Before writing any query logic:
    - Identify which nodes correspond to your test cases
 
 4. **Generate CFG if analyzing control flow**:
+
    ```typescript
    codeql_query_run: {
      queryName: "PrintCFG",
@@ -245,6 +246,7 @@ Instead of writing the full query at once:
    ```
 
 3. **Use find_codeql_query_files** to track all related files:
+
    ```typescript
    find_codeql_query_files: {
      queryPath: '/path/to/Query.ql';
@@ -369,6 +371,7 @@ class ThrowingMethod extends Method {
    ```
 
 3. **Profile the query**:
+
    ```typescript
    profile_codeql_query: {
      query: "/path/to/Query.ql",
@@ -413,11 +416,13 @@ When your query produces correct results but differs from the `.expected` file:
 
 1. **Review the `.actual` file** to verify results are correct
 2. **Accept the results** to update the expected baseline:
+
    ```typescript
    codeql_test_accept: {
      tests: ['/path/to/test/QueryTest'];
    }
    ```
+
 3. **Re-run tests** to confirm they now pass
 
 **Warning**: Only accept results after careful review. Don't blindly accept to make tests pass.

server/src/prompts/tools-query-workflow.prompt.md

@@ -60,7 +60,7 @@ The PrintAST query outputs a hierarchical tree of AST nodes with labels.
 
 **Example AST output structure:**
 
-```
+```text
 TopLevelFunction
 ├── FunctionDeclarationEntry
 ├── Block
@@ -91,7 +91,7 @@ The PrintCFG query outputs control flow nodes and edges.
 
 **Example CFG output structure:**
 
-```
+```text
 nodes
 | node | semmle.label |
 | ... | entry: processData |
@@ -141,7 +141,7 @@ Use the gathered information to inform your query:
 
 ### Pattern 1: Finding All Function Calls
 
-```
+```text
 1. Run PrintAST on your source file
 2. Look for FunctionCall, MethodAccess, or similar nodes
 3. Note the parent/child relationships
@@ -150,7 +150,7 @@ Use the gathered information to inform your query:
 
 ### Pattern 2: Tracing Data Through Functions
 
-```
+```text
 1. Run CallGraphFrom on your entry point function
 2. Identify which functions are called
 3. Run CallGraphTo on sink functions
@@ -159,7 +159,7 @@ Use the gathered information to inform your query:
 
 ### Pattern 3: Understanding Loop Structures
 
-```
+```text
 1. Run PrintAST to find loop constructs (ForStmt, WhileStmt, etc.)
 2. Run PrintCFG on the containing function
 3. Identify back edges that represent loop iteration

server/src/prompts/workshop-creation-workflow.prompt.md

@@ -97,7 +97,7 @@ Decompose the query into 4-8 incremental stages using these strategies:
 
 Standard workshop directory layout:
 
-```
+```text
 workshop-name/
 ├── codeql-workspace.yml      # CodeQL workspace configuration
 ├── README.md                 # Workshop guide with instructions